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Crystal structure determination of camel(Camelus dromedarius)hemoglobin at 2 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PGH PDB ENTRY 2PGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 0.003ml of protein solution with 0.002ml of 45% PEG 3350 in 50mM of phosphate buffer at pH 6.8 with 1 M NaCl equilibrated against 1 ml of reservoir containing the same solution, VAPOR DIFFUSION, HANGING DROP, temperature 293KK
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.759 α = 90 b = 116.782 β = 120.07 c = 52.807 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2009-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 20 94.2 0.0774 5.2 2.43 87740 35552 2.3 2.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 92.4 0.3202 1 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PGH 2 20 31890 31638 3491 94.22 0.23062 0.22358 0.2248 0.29471 0.2966 RANDOM 31.02
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.18 -0.19 -2.92 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_3_deg 16.245 r_dihedral_angle_4_deg 14.883 r_dihedral_angle_1_deg 5.127 r_scangle_it 1.712 r_angle_refined_deg 1.118 r_scbond_it 1.118 r_mcangle_it 0.761 r_mcbond_it 0.435 r_nbtor_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_3_deg 16.245 r_dihedral_angle_4_deg 14.883 r_dihedral_angle_1_deg 5.127 r_scangle_it 1.712 r_angle_refined_deg 1.118 r_scbond_it 1.118 r_mcangle_it 0.761 r_mcbond_it 0.435 r_nbtor_refined 0.287 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.146 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4428 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 172
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling